The general historical setting is accurate: the impact of the French Revolution, the censorships imposed by the Inquisition, Goya's position at court. The characters of Ines & her family, and Lorenzo, are all fictional, as are their storylines. Juan Antonio Llorente, a former priest and Inquisition officer who defected to France and the Bonaparte regime, might have been an inspiration for Lorenzo's character, though.

For Goya, the movie plays kind of fast and loose with the details of his life: he did go deaf due to a mystery illness (possibly Meniere's, polio, botulism, or syphilis), but it was in 1792-3. To my knowledge, Goya didn't run afoul of the Inquisition in those years, either, although his works were beginning to take on darker themes (a small series of paintings on witchcraft and sorcery for the Duke of Osena are a good example). He was married in 1773 to Josefa Bayeu, and they remained married until her death in 1812.

The scope and purpose of the Inquisition by that time was also quite a bit different to what's depicted: it was, by and large, focused on fighting Enlightment ideals via censorship rather than tracking down those accused of "judaizing" (that is to say, it's unlikely that by that time a character in Ines' situation would have been brought up on those charges). In terms of the actual control exerted by the Inquisition in regards to censorship, accounts vary as to how effective or possible their restrictions actually were; it's been suggested that many of their reforms and policies were weren't able to be policed, and so . It's also worth noting that the censors were largely applied to books and other printed reading material rather than visual art.

Also, small thing, but a person who did not repent would not have been garrotted - the garrotting was seen as a "merciful" act before being burned alive for a condemned person who had repented. If (as in the film) Lorenzo did not repent, he would have just been burned.

To actually answer your question: not so much. Goya in Bordeaux (1999) is a better choice for a more historically accurate look at Goya's life.

Sources: Robert Hughes' Goya or Janis Tomlinson's Francisco Goya y Lucientes are both solid and readable biographies to start with, if you're interested in Goya's life and works.

(Also, disclaimer: my focus is Spanish art, so my knowledge of the Inquisition is contextual to that - anyone with a more focused knowledge of the workings of the Inquisition itself, please jump in!)